Life Sciences Commons^™

Development, Evaluation, And Application Of A Novel Error Correction Method For Next Generation Sequencing Data, Isaac Akogwu

Dissertations

Tremendous evolvement in sequencing technologies and the vast availability of data due to decreasing cost of Next-Generation-Sequencing (NGS) has availed scientists the opportunity to address a wide variety of evolutionary and biological issues. NGS uses massively parallel technology to accelerate the process at the expense of accuracy and read length in comparison to earlier Sanger methods. Therefore, computational limitations exist in how much analysis and information can be gleaned from the data without performing some form of error correction.

Error correction process is laborious and consumes a lot of computational resources. Despite the existence of many NGS data error correction …

Ecological And Oceanographic Influences On Leatherback Turtle Behavior And Scyphozoan Jellyfish Distributions In The Gulf Of Mexico, Katrina Aleksa

Dissertations

Leatherback turtles (Dermochelys coriacea) are a wide-ranging, oceanic species that feed exclusively on gelatinous zooplankton. Leatherback have been spotted in the Gulf of Mexico (GoM) for several decades and consistently had a high level of interactions with longline fisheries. However, no quantitative studies have been performed to address the spatiotemporal distribution of these turtles in the GoM. This research determines 1) leatherback movements and high-use areas in the GoM, 2) their association with oceanographic features, 3) the distribution and density of two abundant medusae in the northern GoM and any association with biophysical parameters, and 4) the body …

Evaluating Social Network Dynamics Of Bigg’S Killer Whales (Orcinus Orca) And Vessel Traffic Within A Transboundary Region: Implications For Conservation Management, Courtney Smith

Dissertations

The social lives of animals are defined by group dynamics based on the nature and strength of associations and movements between individuals, often resulting in highly complex and interconnected social networks. However, understanding of how environmental variables may shape this structure is poorly understood. Within the inland waters of Washington State and southern Vancouver Island, British Columbia, mammal-eating Bigg’s (transient) killer whales occur in relatively small, but stable social groups. Group size and occurrence in recent years has increased, coinciding with a growing whale watching industry. Given the central importance of the social network within killer whale population dynamics, such …

Escorting Of Mother-Calf Pairs Of Humpback Whales (Megaptera Novaeangliae) In The Colombian Pacific During The Breeding Season, Natalia Botero Acosta

Dissertations

Humpback whales (Megaptera novaeangliae) belonging to the “breeding G-stock” annually migrate from the Antarctic Peninsula and southern Chile to the southeastern Pacific to reproduce. Associations between mother-calf pairs and escorts were examined in the Gulf of Tribugá, northern Colombian Pacific, using photo-identification and behavioral/spatial sampling. Research hypotheses included: 1. The association between cows and escorts is short-lived, consistent with a male reproductive strategy, 2. The presence of escort(s) elicits a behavioral response from mother-calf pairs and, 3. The patterns of spatial distribution reflect the spatial segregation of maternal females. Groups were classified as mother-calf pairs (Mc), mother, calf …

Signature Whistle Production During A Bottlenose Dolphin Group Integration, Megan S. Broadway

Dissertations

Bottlenose dolphins are an important species of interest because they possess a variety of abilities that are relatively rare in the animal kingdom, one being complex acoustic communication. Signature whistles - distinctive calls that are unique for each individual – are one of the most studied call types, but we know little about how these calls are used in various contexts, such as during an introduction. Looking at the socio-behavioral context in which signature whistles are used is likely the best way of learning how these whistles are used in a particular context (Caldwell, Caldwell, & Tyack, 1990). For this …

A Neuroprotective Role For Mir-1017, A Non-Canonical Mirna, Matthew De Cruz

Master's Theses

miRNAs are post-transcriptional regulators of gene expression, with numerous being involved in neurobiology. Within the human genome a quarter of the identified miRNA loci derive from a class of miRNAs termed tailed mirtrons. Despite the identification of this large population of miRNA, no functional studies have been conducted to identify their role. In this study we examined the highly expressed and deeply conserved Drosophila 3’ tail mirtron, miR-1017, as a candidate to elucidate tailed mirtron functionality. We identified acetylcholine receptor transcripts, Da5 and Da2, as bona fide targets for miR-1017. Interestingly, Da2 is also the host transcript for miR-1017. We …

Combined Effects Of Dissolved Oxygen And Temperature On Aerobic Respiration And Respiratory Recovery Responses Of The Spioniform Polychaete, Streblospio Gynobranchiata, In Relation To Body Size, Alyssa Bennett

Master's Theses

Elevated surface temperatures exacerbate the threat of hypoxia within coastal ecosystems. These two primary stressors likely interact as they elicit opposing physiological responses from marine organisms. Metabolic depression is typically associated with hypoxia, while metabolic rates increase with temperature. Moreover, physiological effects of combined stressors may not be additive. In light of increasing pressures from hypoxia, elevated ocean temperatures, and other stressors within coastal regions, studies need to examine effects of multiple stressors on physiology of coastal organisms.

Mass-specific aerobic respiration (V_O2) was characterized as a proxy for metabolic cost of Streblospio gynobranchiata, at combined levels of …

Morphological, Genetic, And Environmental Characterization Of An Unusual Population Of Isoetes (Isoetaceae, Lycopodiophyta), Shannon L. Walker

Honors Theses

A large and unusual population of Isoetes (Isoetaceae, Lycopodiophyta) in the DeSoto National Forest, Wayne County, Mississippi, was studied to determine if the individuals there represent a new species or if they represent part of the variation of the one primary species of the longleaf pine belt of Mississippi, Isoetes louisianensis, which it most closely resembles. The unusual population and specimens of known Isoetes louisianensis were examined comparatively based on morphology, megaspore ornamentation, examination of habitat characteristics, and phylogenetic analysis of DNA sequence data from the nuclear internal transcribed spacer 1 and 2 (ITS) and the 5.8S ribosomal gene. No …

Impacts Of Oil Exposure During Early Life Development Stages In Sheepshead Minnows (Cyprinodon Variegatus) Under Different Environmental Factors, Danielle Simning

Master's Theses

The release of approximately 5 million barrels of crude oil into the northern Gulf of Mexico during the 2010 Deepwater Horizon oil spill jeopardized estuarine ecosystem health from Texas to Florida. These estuarine habitats, which serve as nurseries for many important fisheries are also prone to rapid fluctuations in environmental stressors such as oxygen concentration, and salinity. The consequence of combined exposure to crude oil and suboptimal environmental factors during early life stage development of fish is still largely unknown. The objective of this project was to investigate the impacts of exposure to crude oil in combination with varying environmental …

Development Of Innate Immunity During In Vitro Differentiation Of Mouse Embryonic Stem Cells, William D'Angelo

Dissertations

Embryonic stem cells (ESCs) hold enormous promise for the goals of regenerative medicine and tissue engineering, and extraordinary progress has been made in defining conditions for differentiation to desired cell types. However, an often overlooked aspect of ESC biology is innate immunity, the ability of cells to detect and respond to pathogens and inflammatory cytokines. A number of recent studies by our lab and others have established that ESCs and other types of pluripotent cells from both mice and humans do not mount typical immune responses to viral or bacterial stimuli. There are also indications that various cell types differentiated …

Effects Of Trophic Relationships On Oyster Reef Restoration Success In The Mississippi Sound, Virginia Robin Fleer

Dissertations

Natural and anthropogenic changes resulting from altered hydrology, hurricanes, variable precipitation, and the BP oil spill have all taken their toll on oyster reefs in Mississippi. In response, oyster reef restoration efforts are currently underway within the Northern Gulf of Mexico. In order to understand why these efforts succeed or fail, it is crucial to consider predator-prey relationships within the context of the trophic dynamics of oyster reefs. Thus, for this dissertation study I integrated a multidisciplinary approach to understanding key trophic interactions affecting oyster recruitment, growth and survival, comprising field sampling, manipulative lab experiments, and individual-based modeling. Spat settlement …

Historical Change Of Seagrasses In The Mississippi And Chandeleur Sounds, Linh Thuy Pham

Dissertations

Seagrasses are important coastal resources facing numerous stressors, and losses have been documented from local to global assessments. Under the broad theme of habitat loss and fragmentation, a study of historical change in total area and landscape configuration of seagrasses in the Mississippi and Chandeleur Sounds was conducted. Mapping data was collated from a multitude of previous projects from 1940 to 2011.

Comparisons of seagrass area among various studies that used different mapping methods can result in overestimation of area change and misleading conclusions of change over time. The vegetated seagrass area (VSA) data were generalized to a common resolution …

Salinity Tolerance Of Gambusia Affinis, Sarah Rubelowsky

Honors Theses

Developmental plasticity refers to changes during development as a result of environmental contributions. Salinity is a varying environmental condition in freshwater and estuarine habitats that can mediate developmental plasticity in Gambusia affinis, which can increase their tolerances as an invasive species. For my study, estuarine and freshwater populations of Gambusia affinis were sampled in March of 2017 using dip nets. Both populations were then brought back to the laboratory where pregnant females were acclimated to three different salinities (0‰, 15‰, 25‰) until they gave birth. I predicted that the estuarine population of Gambusia affinis would have a greater salinity tolerance …

An Examination Of The Influence Of Social Physique Anxiety On Effort And Exercise Participation In College Students, Trellony M. Irwin

Honors Theses

The purpose of this study was to investigate whether an individual’s perception of others influenced exercise participation and effort in women and men participants involved in exercise classes in a campus recreation facility. The study consists of a survey that utilizes the Social Physique Anxiety Scale, the Ratings of Perceived Exertion (RPE) Scale, and demographic information. Results revealed that participants’ social physique anxiety accounted for roughly 30% of the variance in self-reported physical activity. However, when it came to participant effort during the group exercise classes, there was only roughly 2% variance between social physique anxiety and RPE. Further, the …

Effects Of Temperature On Growth And Molting In Blue Crabs (Callinectes Sapidus) And Lesser Blue Crabs (Callinectes Similis), Abigail Ann Kuhn

Master's Theses

Temperature can exert impacts on many processes in ectotherms. With global temperatures rising due to climate change, many ectothermic species may exhibit changes in growth rates and size at maturity, and these changes can have population-level effects. Predicting responses of species to climate change will require not only knowledge of thermal tolerance limits, but also effects of temperature change on growth rates and other life history parameters. For arthropods that exhibit discontinuous growth (i.e., molting), this includes both intermolt period and growth per molt. Previous laboratory and field experiments suggest that temperature affects both intermolt period (IMP) and growth per …

Effects Of Wave Action On The Structure Of Fish Assemblages Across An Exposure Gradient, Lauren Liddon

Master's Theses

Disturbance affects the function and diversity of ecosystems. Increased wave exposure to salt marsh can disturb sediments and cause a loss of habitat. The purpose of this study was to explore the effects of increased wave exposure on diversity, abundance, and functional ecology of estuarine fishes. If increased wave exposure is acting as a disturbance to these habitats, ecological theory (Intermediate Disturbance Hypothesis) predicts that diversity will peak at intermediate frequencies and intensities of disturbance. Fish were sampled from 10 sites monthly for 6 years. The sites were assigned to different exposure categories (Open, Intermediate, and Sheltered) using an exposure …

Environmentally-Driven Variation In The Population Dynamics Of Gulf Menhaden (Brevoortia Patronus), Grant D. Adams

Master's Theses

Gulf Menhaden (Brevoortia patronus) is an abundant forage fish distributed throughout the Northern Gulf of Mexico (NGOM). Gulf Menhaden support the second largest fishery, by weight, in the United States and represent a key linkage between upper and lower trophic levels. Variation in the population dynamics can, therefore, pose consequences for the ecology and economy in the NGOM. Here we aim to understand variation in the individual and population dynamics of Gulf Menhaden throughout ontogeny and how such variation relates to environmental processes. We utilized a suite of fishery-dependent and –independent, remote sensing, modeled, and in situ data …

Evidence Of Multidecadal Recruitment In The Ocean Quahog, Arctica Islandica In The Western Atlantic Ocean, Sara M. Pace

Master's Theses

Ocean quahogs (Arctica islandica) are the longest-lived, non-colonial animals known today, with a maximum life span exceeding 500 years. Limited information is available regarding recruitment, making the sustainable management of this valuable fishery a challenge. The objective of this research was to describe the age structure and growth rates for four populations of ocean quahogs from the mid-Atlantic stock to evaluate long-term recruitment trends. Clams were sectioned for age estimation to develop population age frequencies. Initial colonization began approximately 175-250 years ago depending upon site. All sites experienced an increase in recruitment beginning in the late 1800’s to …

An Ecological Examination Of Johnson Bayou (Pass Christian, Ms) With A Reproductive Histological Analysis Of Rangia Cuneata, And A Comparative Morphological Study Of The Foot And Shell Of Rangia Cuneata And Polymesoda Caroliniana, Brandon Drescher

Dissertations

Johnson Bayou is an estuarine system located in Pass Christian, MS. Research involved a biotic and abiotic examination of Johnson Bayou, resulting in the identification of numerous species of plants and animals, including Rangia cuneata (Mactridae) and Polymesoda caroliniana (Cyrenidae), sympatric species of infaunal bivalves. Environmental factors (e.g., water temperature, salinity) were measured over three years to describe the system from an abiotic standpoint, and used in a qualitative and quantitative reproductive histological study on R. cuneata. Results revealed differences in timing of gamete production and spawning between three subpopulations of this species. Sediment samples taken from the study …

Taxonomy And Systematics Of Plagioporus (Trematoda), With Descriptions Of 10 New Species From Freshwater Fishes Of The Nearctic, Thomas John Fayton

Dissertations

The Opecoelidae Ozaki, 1925 is one of the largest families of digenetic trematodes of fishes. While the family is mostly marine/estuarine, invasion of freshwater hosts has occurred at least two times. The only representative freshwater plagioporine sequenced to date is Plagiocirrus loboides Curran, Overstreet, & Tkach, 2007, which previous phylogenetic analyses resolved as being related to deep water marine opecoelids. The taxonomy of the freshwater plagioporines, particularly Plagioporus, has long been confused; homoplasy is rife within the family and has complicated the delineation of species and genera, and the freshwater species from marine forms. Here, I hypothesize that the …

Solution Of Pdes For First-Order Photobleaching Kinetics Using Krylov Subspace Spectral Methods, Somayyeh Sheikholeslami

Dissertations

We solve the first order reaction-diffusion equations which describe binding-diffusion kinetics using a photobleaching scanning profile of a confocal laser scanning microscope approximated by a Gaussian laser profile. We show how to solve these equations with prebleach steady-state initial conditions using a time-domain method known as a Krylov Subspace Spectral (KSS) method. KSS methods are explicit methods for solving time- dependent variable-coefficient partial differential equations (PDEs). KSS methods are advantageous compared to other methods because of their stability and their superior scalability. These advantages are obtained by applying Gaussian quadrature rules in the spectral domain developed by Golub and Meurant. …

The Effect Of Normal Helmet Degradation In Division I Football Players Over The Period Of One Half Of A Competitive Season, Matthew Mcmullan

Honors Theses

The purpose of this thesis is to evaluate the effect of normal helmet use by athletes from a Division I football team over the period of the first half of a competitive season upon the impact performance characteristics as measured by peak g values obtained through the application of the NOCSAE drop impact testing protocol. The goal of this research is to determine if one half of a season is enough time exposure to result in a significant decrease in a helmet’s performance quality. This study tracks changes in performance in overall function, as well as the function of each …

Elucidating The Interplay Between Sodium Selenite On The Tick Amblyomma Maculatum Selenoprotein Gene Expression, Afnan M. Beauti

Honors Theses

Selenium (Se) is an element recognized as an essential micronutrient in eukaryote organisms. Selenoproteins contain selenium as selenocysteine, the 21st amino acid. Selenium plays a role in cell growth and functioning. At low concentrations, it can induce growth and at high concentrations, it can cause a cell to stop growing and potentially have toxic effects on the cell and organism. When selenium levels are high, oxidative stress results by the production of reactive oxidative species. Selenoproteins, however, can aid the antioxidant response in the cell. Ticks are arthropods of interest, as they are one of few that contain many selenogenes, …

Effects Of Temperature Gradient, Substrate Composition, And Canopy Cover On The Spatial Distribution Of Topminnow Species: Fundulus Notatus And Fundulus Olivaceus, Austin M. King

Honors Theses

Hybrid zones are locations where two interbreeding species coexist and hybridize. The spatial distribution of ecologically similar species is of primary interest in understanding the formation and stability of hybrid zones. These hybrid zones are of significance as they allow for insight into how speciation occurs naturally within the environment. A variety of factors may play a role in determining the spatial distributions of species within hybrid zones. Examples of these factors include variations in temperature gradients, substrate composition, and changes in canopy cover. Fundulus olivaceus and Fundulus notatus are generally found within upstream and downstream habitats respectfully. These habitats …

Anxiety-Like Behaviors And C-Fos Expression In Adult Zebrafish: Effects Of Housing Conditions, Alcohol And Caffeine, Adam Douglas Collier

Dissertations

Alcohol abuse is the third largest risk factor for disease world, responsible for an estimated 3.3 million deaths each year. The concomitant ingestion of alcohol and caffeine is hypothesized to increase risk factors associated with alcohol use alone by reducing subjective effects of intoxication. The zebrafish (Danio rerio) has recently garnered attention from researchers as an effective pre-clinical in-vivo animal model in behavioral pharmacology research, largely due to small size, low-cost and ease of drug delivery. A number of studies have reported the effects of alcohol and caffeine on zebrafish behavior at a variety of doses. However, the …

Characterization Of Andrenocortical Tissue Morphology, Histology, And Steroid Synthesis Among Finetooth (Carcharhinus Isodon), Blacktip (Carcharhinus Limbatus), Atlantic Sharpnose (Rhizoprionodon Terraenovae), And Bonnethead (Sphyrna Tiburo) Sharks, Danielle Elizabeth Bailey

Master's Theses

Adrenocortical (interrenal) tissue is composed of steroidogenic cells that produce corticosteroids involved in the stress response and hydromineral balance. Previous research characterizing the elasmobranch interrenal suggests that the number of interrenal bodies that produce the single primary corticosteroid, 1a-hydroxycorticosterone (1a-OHB), varies among species. However, potential species-specific differences in the amount of interrenal tissue and major steroid products produced have been understudied. To address this critical gap in our understanding of elasmobranch biology, this study examined interrenal morphology, cell structure, steroidogenic enzyme distribution (3bHSD), and steroid production in four shark species: Finetooth Carcharhinus isodon, Blacktip Carcharhinus limbatus, Atlantic Sharpnose …

Disorder In Cysteine-Rich Granulin-3 And Its Implication In Alzheimer Disease, Gaurav Ghag

Dissertations

Granulins (GRNs) are a family of small, cysteine-rich proteins that are generated upon proteolytic cleavage of their precursor, progranulin (PGRN) during inflammation. All seven GRNs (1 – 7 or A – G) contain twelve conserved cysteines that form six intramolecular disulfide bonds, rendering this family of proteins unique. GRNs play multiple roles and are involved in a myriad of physiological as well as pathological processes. They are known to a play role in growth and embryonic development, wound healing, and signaling cascades as well as in tumorigenesis. They are also implicated in neurodegenerative diseases like frontotemporal dementia (FTD), Alzheimer disease …

Age, Growth, And Reproduction Of Vermilion Snapper (Rhomboplites Aurorubens) In The North-Central Gulf Of Mexico, Trevor Dalton Moncrief

Master's Theses

Vermilion Snapper is a commonly harvested species of reef fish in the northern Gulf of Mexico (GOM). It supports both a large commercial and popular recreational fishery, however knowledge of this fish’s life history is limited spatially. Non-linear curve fitting was used to estimate growth parameters and Akaike information criteria (AIC) was used to determine relative model fit. The 2-parameter von Bertalanffy growth function provided the best model fit and lowest AIC score. Histological examination indicated that Vermilion Snapper are batch spawners with asynchronous oocyte development. Additionally, 17% of Vermilion Snapper in the actively spawning phase containing 24 hour POF’s …

Life History Of The Non-Native Invasive Red Lionfish (Pterois Volitans) In The Northern Gulf Of Mexico, Alexander Q. Fogg

Master's Theses

Invasive Red Lionfish (Pterois volitans) were first detected in the northern Gulf of Mexico (nGOM) in 2010 and since then their numbers have increased dramatically. From 2010 to 2015, more than 15,000 Red Lionfish were collected opportunistically from the nGOM for this study. Length and weight relationships differed significantly among ecoregions by sex and there was clear sexual dimorphism in size with males being larger and heavier. Red Lionfish age ranged from 0-4.5 years old and males achieved greater growth rate (K) and asymptotic maximum lengths (L_inf) compared to females and these parameters were also different …

Characterization Of P43lgrn-3, Kelly G. Hill

Honors Theses

Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by extensive memory loss and cognitive deficits, which occur due to severe neuronal loss. Two hallmark lesions, intracellular neurofibrillary tangles composed of hyperphosphorylated tau and extracellular neuritic plaques formed by the aggregation of amyloid-β (Aβ), are responsible for the progressive neuronal loss seen in AD brains. Neurotoxic Aβ aggregates are also known to cause inflammation within the brain. It has recently come to light that severe and acute inflammation, such as seen in traumatic brain injury (TBI), may also lead to AD-type dementia. This has raised the question whether some of …